I am having trouble using calibre to send books to the nook. Just got it today. I managed to send one book over but now it apparently doesn't recognize that the eBook is connected. Does anyone have any ideas

Make sure you properly eject/unmount the device before you physically unplug it from the USB port. That makes sure that any pending disk writes that are still buffered are actually written to the device. If they aren't you could have a corrupt file there, which the system can't read and deal with. In Calibre, you can use the eject icon where it shows the device. In Linux, you can use your file manager to unmount, or if it appears on your desktop, you can do it there. In Windows 7 you right click on the device, and select eject. Earlier versions of Windows allowed you to click on an icon in the system tray to "safely remove device." I haven't a clue how to do it with a Mac.